Wednesday, May 11, 2016

What Are They Teaching at Washington University? S. Joshua Swamidass and the Chimp-Human Divergence

Stunning Evidence For Common Ancestry

I once had a rare and valuable baseball card I wanted to sell. I placed an ad and was shortly contacted by a collector. But to my dismay he wasn’t interested. He had probably looked at hundreds of baseball cards and it only required one look for him to know that my treasured card held no value for him. He did not attempt any negotiating tricks, just a polite “thank you” and off he went. I would have felt better about the encounter if he had tried to haggle down the price. For I would have had the comfort of knowing my card held at least some value. Instead, there was no price discovery—apparently the card was worthless.

I too am a collector of sorts. And like that baseball card collector I have looked at hundreds of specimens. No matter how unlikely the source or the venue, I will go there and have a look. And in short order, I will know exactly what I am looking at, and if there is any value there. But unlike the baseball card collector, my subject is not something you can touch. What I am interested in are the arguments and evidences for evolution. Ever since Darwin, evolutionists have insisted that their idea is undeniable—beyond all reasonable doubt. I find that complete certainty to be fascinating. So I search, find, analyze and categorize every justification and explanation for that conclusion that I can find.

My goal is to find the strongest, most powerful, such arguments and evidences, and to understand how we can have such certainty. This brings us to S. Joshua Swamidass’s recent article, Evidence and Evolution where Swamidass explains, in typical fashion, that the evidence for evolution is powerful and compelling. Swamidass describes the evidence as stunning. As a professor in the Genomic Medicine Division at Washington University, Swamidass deserves to be listened to. This is definitely a specimen I want to have a look at.

In his article, Swamidass’ focus is human evolution. Evolutionists believe that we humans evolved from a small ape-like creature and that our closest relative on the evolutionary tree is the chimpanzee. The chimpanzee must be our closest relative, they reason, because the chimp’s genome is closest to ours, and according to evolution, genetic mutations are the fuel behind evolutionary change.

The problem with this reasoning is that the chimpanzee is not very similar to humans according to many other measures. There are enormous differences between the two species. Simply put, from an evolutionary perspective the genetic data are not congruent with the other data. Swamidass’ evidence will need to overcome this obvious problem.

But that’s not all.

The basic idea of humans arising via a long series of genetic mutations is, itself, not indicated by the science and unlikely to say the least. Remember, the mutations have to be random. According to evolution, you can’t have mutations occurring for some purpose, such as creating a design. And natural selection doesn’t help—it cannot induce or coax the right mutations to occur. This makes the evolution of even a single protein, let alone humans, statistically impossible. So this is another enormous problem Swamidass’ evidence will need to overcome.

But that’s not all.

The incredible designs in the human body are not the only thing those random mutations have to create—they will also have to create human consciousness. Evolutionists may try to explain consciousness as an “emergent” property that just luckily arose when our brain somehow evolved. Or they may try to explain that consciousness is really no more than an illusion. But these are just more demonstrations of anti realism in evolutionary thought. Evolutionary theory constructs mechanisms and explanations that do not correspond to the real world. So this is another problem Swamidass will need to overcome.

But that’s not all.

In recent decades the genomes of humans and chimps have been determined, and they make no sense on evolution. One of the main problems is that the genes of the two species are almost identical. They are only about 1-2% different and, if you’re an evolutionist, this means you have to believe that the evolution of humans from a small, primitive, ape-like creature was caused by only a tiny modification of the genome.

This goes against everything we have learned about genetics. You can insert far greater genetic changes with far less change arising as a consequence. It makes little sense that tiny genetic changes could cause such enormous design changes to occur. This is yet another problem for Swamidass to overcome.

But that’s not all.

Not only is evolution limited to tiny genetic modifications to create the human, but the majority of those modifications would have had to be of little or no consequence. Here is how a 2005 paper on the chimpanzee-human genome comparisons put it:

In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles.

The paper is written from an evolutionary perspective, assuming that humans and chimpanzees share a common ancestor. Given that a priori assumption, they were forced to conclude that most of the mutations affecting protein-coding genes led to “neutral and slightly deleterious alleles.” So not only are evolution’s random mutation resources meager, in terms of both quality and quantity as explained above, but even worse, those mutations mostly led to “neutral and slightly deleterious alleles.” This is no way to evolve the most complex designs in the world and it is yet another problem for Swamidass to overcome.

But that’s not all.

The supposed divergence rate between chimps and humans also has an unexplainable variation towards the ends of most chromosomes. This is another problem that seems to make no sense on evolution, which Swamidass must explain.

But that’s not all.

This supposed divergence rate between chimps and humans also has an unexplainable variation that correlates with chromosomal banding. Again, this makes no sense on evolution. Why should the chimp-human divergence vary with the banding pattern? Evolutionists have only just-so stories to imagine why this would have happened, and it is another problem for Swamidass to address.

But that’s not all.

This supposed divergence rate between chimps and humans is not consistent with the supposed divergence rate between the mouse and rat. The mouse-rat divergence is about an order of magnitude greater than the chimp-human divergence. And yet the mouse and rat are much more similar than the chimp and human. It makes no sense on evolution. In fact, before the rat genome was determined, evolutionists predicted it would be highly similar to the mouse genome. As one paper explained:

Before the launch of the Rat Genome Sequencing Project (RGSP), there was much debate about the overall value of the rat genome sequence and its contribution to the utility of the rat as a model organism. The debate was fuelled by the naive belief that the rat and mouse were so similar morphologically and evolutionarily that the rat sequence would be redundant.

The prediction that the mouse and rat genomes would be highly similar made sense according to evolution. But it was dramatically wrong.

Another approach is to ignore the morphological similarities and reason from the number of generations available to produce the genomic differences between the mouse and rat. The mouse-rat divergence date is estimated by evolutionists to be older than the chimp-human divergence date. Furthermore, the lifespan and generation time for mice and rats are much shorter than for chimps and humans. From this perspective, and given these two effects, one would conclude that the mouse-rat genetic divergence should be much greater—at least two orders of magnitude greater—than the chimp-human genetic divergence. But it isn’t. It is only about one order of magnitude greater.

So either way the mouse-rat comparison does not help to explain things and is another problem for Swamidass to explain.Swamidass arguments and evidences

The science makes no sense on evolution. If we begin by assuming chimps and humans share a common ancestor, we end up with all kinds of contradictions and failures. So what exactly are Swamidass’ arguments and evidences? How is it that he is so certain? What is it in the data that he finds to be so stunning? And most importantly, how does he resolve the above problems?

Well, he doesn’t.

Astonishingly, Swamidass doesn’t even mention the above problems. It is as though they don’t exist. After some stories and high claims of certainty, here is what Swamidass says:

As predicted by common ancestry, human and chimpanzee genomes are extremely similar (greater than 98% similarity in coding regions), much more similar than we would expect without common descent. Remarkably, just as predicted by the fossil record, humans are about 10 times more genetically similar to chimpanzees than mice are to rats.

First, the high chimp-human genomic similarity was not predicted by common ancestry. No such prediction was made and no such prediction is required by common ancestry. Common ancestry would be just fine with very different levels of similarity than 98-99%. In fact, this high similarity makes no sense on evolution, for several of the reasons given above.

Swamidass’ claim that this evidence is a stunning confirmation of common ancestry is utterly at odds with the science. It is in stark contrast to the scientific facts.

Second, Swamidass’ claim that mouse-rat divergence, compared with the chimp-human divergence, is “just as predicted by the fossil record” is also blatantly false. While evolutionists can always combine various explanatory mechanisms to rationalize just about any comparison, that does not make for stunning evidence that is “just as predicted.”

Finally, the real strength of Swamidass’ argument lies in its metaphysics. The professor states that the chimp-human genome comparison is “much more similar than we would expect without common descent.”

Without common descent?

The evolutionist has just made an unbeatable (and unfalsifiable) argument.

This is not science. Swamidass’ claim about what is and isn’t likely “without common descent” is not open to scientific scrutiny.

Scientists, qua scientists, do not have knowledge of all possible explanations for the origin of life. This is why scientists, qua scientists, make statements about theories, not about the complement of a theory. A scientist cannot know that something is unlikely “without” his theory. That implies knowledge of all other possible theories. And that knowledge does not come from science.

This is the strength of Swamidass’ argument. Notice that with this metaphysical knowledge, all of the scientific problems melt away. No wonder he does not address them. They are inconsequential. At worst, they are simply interesting puzzles. The truth of the matter is already known.

If Swamidass is correct then, yes, of course, the genomic data must be strong evidence for common ancestry. But it all hinges on his metaphysics. This is not about science. It never was.

[Ed; Removed sentence about the orangutan, 1-Mb segments section, and the gene functionality section. Please see the followup article here.]

A Closer Look At Human/Chimp Similarities and Differences – videohttps://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1134643976548534/?type=2&theater

also of note:

As to the implausibility of changing one creature of trillions of cells into another creature of trillions of cells, here are a few notes:http://www.uncommondescent.com/intelligent-design/the-simple-steps-that-made-us-human/#comment-606171

There is no such thing as "THE Scientific Method."If you go to science fairs or read scientific journals, you may get the impression that science is nothing more than "question-hypothesis-procedure-data-conclusions."

But this is seldom the way scientists actually do their work. Most scientific thinking, whether done while jogging, in the shower, in a lab, or while excavating a fossil, involves continuous observations, questions, multiple hypotheses, and more observations. It seldom "concludes" and never "proves."

There isn't any way to scientifically test the claim that humans and chimps share a common ancestor. The only way to test the claim is to assume it happened and then look for what you think would be confirming evidence.

Why Joke? Testing to see if the paint is wet doesn't require a how or why.

By your logic every hypothesis for Intelligent Design needs to test how and why the Design was done yet you scream it's only about detecting design!! That makes you a big fat hypocrite as well as being amazingly scientifically ignorant.

We know it was deigned because there aren't any materialistic processes that can produce it

You don't know that Joke. You assert it despite all the evidence to the contrary. ID has zero positive evidence of its own to offer.

AND it matches the design criteria.

We also have no before-the-fact design criteria for biological life. All you've got is stupid arguments by analogy. "This superficially resembles a human design so it must BE designed by my chosen supernatural entity!"

We know it was deigned because there aren't any materialistic processes that can produce it

You don't know that, Joe

Yes, we do. You don't have anything to explain what we observe

You assert it despite all the evidence to the contrary.

What evidence to the contrary? How can we test the claim that natural selection and drift produced ATP synthase?

ID has zero positive evidence of its own to offer.

The genetic code. Biological information. All biological systems and subsystems. Genetic algorithms which model evolution by design. The laws that govern the universe. And much more.

We also have no before-the-fact design criteria for biological life.

More gibberish. There is a design criteria as Dr Behe laid out:

"Our ability to be confident of the design of the cilium or intracellular transport rests on the same principles to be confident of the design of anything: the ordering of separate components to achieve an identifiable function that depends sharply on the components.”

So if we observe that and there aren't any materialistic explanations, we infer design. What Behe described is the POSITIVE case.

What is the positive case for evolutionism? Darwin already admitted that to falsify it requires proving a negative. But no one ever said anything about any positive criteria.

LOL! Joe can't stop. Despite his tremendous girth he's a small, petty, failure of a man. Screaming obscenities and making impotent threats against strangers on the internet is the only way he knows to feel better about himself.

When people talk about the Scientific Method, I get a little confused since I cam across different definitions of the Scientific Method in different textbooks I used in my classrooms. I'm thinking that maybe there is no canonical scientific method.

"Biology, The Study of Life" by Sachraer and Stolzte says that the Scientific method consists of defining the problem, formulating a hypothesis, testing the hypothesis, observing and measuring, analyzing and drawing conclusions, and reporting observations.

"Biology" by Mills and Levine lalks about science and how scientists work.Science involves evidence based on observation, interpreting the evidence, and explaining the evidence..Scientists work by studying the evidence, forming a hypothesis, setting up a controlled experiment, recoding and analyzing the results, drawing conclusions, publishing and repeating the investigation, If a controlled experiment isn't possible, then they substitute field work.

"Evironmental Science" by Karen Arms says that there are scientific methods.That is, there is more then one method. These can include observing, hypothesizing and predicting, experimenting, organizing and interpreting information, using graphs and sharing information, and communicatiing results.

"Modern Earth Science" by Sager, Rancey, Phillips and Watenpaugh also discusses different scientific methods. They include stating the problem, gathering information, forming a hypothesis, testing the hypothesis by experiment, and stating a conclusion.

"Earth Science" by Spaulding and Namowitz talks about scientific thinking. This includes observations, gathering evidence, formulating a hypothesis, skeptical questioning, analyzing what is known, and using math and technology. The scientific methods of inquiry involve collecting data, analyzing the data, testing the hypothesis, and peer review in scientific journals.

"Holt Science and Technology: Earth Science" says that scientific methods do not have a set procedure, but they can include some or all of the following, asking a question, forming a hypothesis, testing by controlled experiment, making observations, keeping records, analyzing results, drawing conclusions, and communicating results.

Your buddy Joe says we can't make hypotheses because that would be assuming the thing we want to test.

Liar, I never said that you cannot make hypotheses. I said you cannot assume the very thing you are testing and then say that you are testing it.

That said there aren't any testable hypotheses for natural selection and drift producing ATP synthase nor any other biological system. So if they are a necessity then that proves Timmy's position is total nonsense.

Hello, I will point out that you did not answer my question in the article. I asked, "Why are rats and mice 10x more different than humans? What design principle predicts this?" It is true, by other measures, chimps and humans are more different then 1.2%. But in all these measures, rats and mice are more than 10x more different. This makes sense in light of common descent, which is why Michael Behe (for example) is a theistic evolutionist, just like me. The problem is not my metaphysics. I am a Christian just like you. Try again. Curious what you can come up with for my real question.

My case is simple. Evolution explains this easily. Design has no explanation, at least that I know of. This is so convincing that Micheal Behe, a leading light in the the ID movement, agrees with me here. This is why he is a theistic evolutionist.

ID is widely perceived as anti-evolution, even though Michael Behe is a theistic evolutionist. I'm just arguing there is strong evidence for common descent. In fact, it was reading Behe' books that convinced me that common descent was likely true.

I encourage you to read in detail the links to BioLogos at the original article, which answer you questions in detail. You can find my original at my website (http://swami.wustl.edu). In particular, the series on egg yolks is enlightening, entertaining, and plays out exactly how that test can be made. Biology takes deep expertise, so it will probably take you a few hours to learn the salient points. It should be fun. Let me know what you think!

Of course, I welcome Behe. He is one of my favorite people in the ID movement. I just doubt science more than him. He is so certain that science can detect God's influence. I'm am very skeptical that science could ever do that. I just do not trust it as much as he does.

you did not answer my question in the article. I asked, "Why are rats and mice 10x more different than humans?

I did not see that question in there. I did see, however, that you made a claim. You stated that the chimp and human genomes are “much more similar than we would expect without common descent.” I don’t know how you concluded that, but it is not from science.

The problem is not my metaphysics. I am a Christian just like you. Try again.

Well you did not inform your readers of a host of scientific problems, and your argument hinged on your metaphysical claim. You say “The problem is not my metaphysics.” I have no problem with that—I’ll grant you your metaphysics. But you were claiming in your article that your conclusions were scientific, and that they were compelling. That is not accurate—your conclusions hinged on your metaphysics, not the science. That was my point.

Thank you for the respectful reply. First, I offer out that I am always available for comment if you ever post about me again. I treat respectful people with respect, and aim for dialogue, not diatribes.

This comes down to two issues, as far as I see it.

1) We do not agree about what science is. The problem is not metaphysics (where we agree) but our philosophy of science, where we sit at opposite ends of the room.

2) The core of my point is still left untouched. Design can explain why humans are chimps are similar. It can not (as far as I can tell) explain why humans and chimps are 10x more similar than rats and mice. Of course, it is not just rats and mice. I wide range of species that most creationists accept are products of micro-evolution are much more divergent than humans and chimps. Evolution has an explanation for this puzzle, but I am waiting to hear a compelling design explanation.

but our philosophy of science, where we sit at opposite ends of the room.

Well I wrote the lengthy OP (above) to explain the science. I wonder why you would differ on those points? In your article, you stated: “Remarkably, just as predicted by the fossil record, humans are about 10 times more genetically similar to chimpanzees than mice are to rats.” That was a short comment without explanation. I explained why there is no such prediction from the science (fossil record, generation time, etc.). So I’m left wondering, if we are sitting at opposite ends of the room, and our philosophy of science is so different, what exactly is yours? How is it that the many scientific problems I pointed out do not matter so much?

The core of my point is still left untouched. Design can explain why humans are chimps are similar. It can not (as far as I can tell) explain why humans and chimps are 10x more similar than rats and mice. Of course, it is not just rats and mice. I wide range of species that most creationists accept are products of micro-evolution are much more divergent than humans and chimps. Evolution has an explanation for this puzzle

Well actually this evidence you cite causes a lot of problems for evolution. The evidence is not a “stunning” confirmation of evolution as you say it is. And I don’t see how it would be accurate to say that evolution “has an explanation for this puzzle.” For instance, evolutionists originally predicted that rats and mice would have genomes even more similar than chimps-humans. The differences were a surprise. And secondly, from a drift perspective, the rat-mice alignments should show greater differences than they do, given the short generation time and longer time since divergence. But there are several other scientific problems as well, as explained in the OP. So I don’t think it is accurate to say that evolution “has an explanation for this puzzle.”

The core of my point is still left untouched. Design can explain why humans are chimps are similar. It can not (as far as I can tell) explain why humans and chimps are 10x more similar than rats and mice.

There is a lot to unpack here. First, when evolutionists say the design cannot explain X, typically they are relying on an understanding of X which is from an evolutionary perspective. Their scientific judgments are theory-laden.

For instance, a strong bias that evolution enforces is for the genome. Evolution is fueled by genetic mutations. They are the raw material for evolution, so evolution promoted and mandated a high-view of the genome. Simply put, the genotype determines the phenotype. The rest of cell is a bunch of machinery supporting the genome.

Then evolutionists look at the chimp-human genomes, and the rat-mouse genomes, and comparisons, and say it doesn’t make sense on design.

But this is looking at everything through evolutionary lenses. I would say both design and evolution cannot make sense of the chimp-human genetic similarities. But what that tells me is that we don’t fully understand biology. There is something more going on than merely structural and regulatory genes creating the organism. Or if they are doing it, they are doing it in a way we don’t understand. A 1-2% difference doesn’t make sense given the enormous differences between the chimp and human. But then again, I never made a chimp or a human.

The core of my point is still left untouched. Design can explain why humans are chimps are similar. It can not (as far as I can tell) explain why humans and chimps are 10x more similar than rats and mice.

Evolution is always based on contrastive reasoning. Darwin’s work, and ever since Darwin (and before Darwin all the way back to the Epicureans), evolution has been one long referendum on design and creation. The world doesn’t make sense, so it must have evolved. The Epicureans referred to “randomly swerving atoms.” Now we have randomly mutating nucleotides. The Epicureans referred to the evils, inefficiencies and dysteleology of the world. Today evolutionists do the same. Nothing has changed in this argument. We have no idea how mutations could have created the species. In fact, everything we do know argues against it. But it must be true. This is not about science.

This is really a lot here, and I am happy to explain it, going over you article in detail. You have PhD in science and have been studying this a lot, so I am hopeful you might understand where I am coming from. Even if you we would not agree in the end.

A comment thread, however, is the not the right place for a technical discussion about the genetic details.

I'll be in Azusa in July for the ASA meeting. That is in your neighborhood. Drive out to see me, I'll buy you a beer, and we can talk more.

JoshuaThe answer to the puzzle may be other biochemical difference other than the genome. There are large differences in the timing expression and alternative splicing sequences between humans and chimps. Proteins are modified by alternative splicing and 70 to 90% of the human genome is alternatively spliced vs half for a chimp. So that same DNA can produce a very different protein by way of the spliceosome. I can supply papers on this subject if you would like. Unfortunately the source of the splicing codes is not understood at this point but almost certainly are not formed from a stochastic processes. The hypotheses that man evolved from chimps via a stochastic process is almost certainly false.

S Joshua Swamidass, the fossil record is not as conducive to gradualism as you have been 'misled' to believe:

“A number of hominid crania are known from sites in eastern and southern Africa in the 400- to 200-thousand-year range, but none of them looks like a close antecedent of the anatomically distinctive Homo sapiens…Even allowing for the poor record we have of our close extinct kin, Homo sapiens appears as distinctive and unprecedented…there is certainly no evidence to support the notion that we gradually became who we inherently are over an extended period, in either the physical or the intellectual sense.”Dr. Ian Tattersall: – paleoanthropologist – emeritus curator of the American Museum of Natural History – (Masters of the Planet, 2012)

Scientific study turns understanding about evolution on its head - July 30, 2013Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form.Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories.,,,Dr Matthew Wills said: "This pattern, known as 'early high disparity', turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn't a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.",,,Author Martin Hughes, continued: "Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on.Co-author Dr Sylvain Gerber, added: "A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,,http://phys.org/news/2013-07-scientific-evolution.html

It should be obvious to all but dirt worshippers that the high genetic similarity between humans and chimps is precisely what one would expect from an intelligent design perspective. Human designers too reuse their tried and tested designs every day. In fact, object-oriented design is a staple of software engineering. SE could not exist without it. It enforces a class hierarchy. As I wrote in a comment on the previous article, intelligent design predicts that the genome must be organized in a strict hierarchy. This "genomic tree of life" is an unmistakable sign of intelligent design and this is precisely what genomic researchers are finding.

I can only laugh at the beauty of it all and at the utter stupidity of evotards and their cretinous little "theory". Evotards have one thing in common with voodoo practitioners: they are both deeply superstitious.

"It should be obvious to all but dirt worshippers that the high genetic similarity between humans and chimps is precisely what one would expect from an intelligent design perspective. Human designers too reuse their tried and tested designs every day. In fact, object-oriented design is a staple of software engineering. SE could not exist without it. It enforces a class hierarchy. As I wrote in a comment on the previous article, intelligent design predicts that the genome must be organized in a strict hierarchy. This "genomic tree of life" is an unmistakable sign of intelligent design and this is precisely what genomic researchers are finding."

Rhertoric aside, I agree with the main points here. The assumptions that go into the belief of Human descent are staggering. But then again, we are ultimately dealing with people's religious beliefs therefore logic will not reign supreme at the end of the day.

Rhertoric aside, I agree with the main points here. The assumptions that go into the belief of Human descent are staggering. But then again, we are ultimately dealing with people's religious beliefs therefore logic will not reign supreme at the end of the day.

The irony / hypocrisy is that we are the ones who get the blame. They bring in religion, and we get the blame for it.

I could not believe the assertions they make in it. It has basically political undertones for an atheist agenda. It also basically says that people who are critical of evolution's capacity to account for the origin of life basically are against fighting diseases (or so it seems to imply) or the limited adaption of species. The straw men are staggering.

I checked out your link, it was a source of many good laughs. If you want to be really entertained try clicking on the links at the bottom of the page. On one the writer, Michael Le Page, is still promoting the peppered moths as an example of observable evolution. Too funny.

Pretty good and well wrote.I like the point about how if we evolved from a common ancestor we should have MORE difference in dna. the idea of close likeness in dNA should not be welcomed.

This creationist believes we do have the primate body. We alone don't have a body type for ourselves.This because we alone have our identity in Gods image. Animals identity is in thier kind and so thier body types represent this.We are renting a body type in order to stay in the spectrum of restrictions on the common blueprint for biology.SO I welcome humans being 99'999% alike in DNA with apes/orangs/chimps.We do have ape bodies.We alone in nature are like this.The best beings alone have bodies like other beings.No one else can say that.

Pretty good and well wrote.I like the point about how if we evolved from a common ancestor we should have MORE difference in dna. the idea of close likeness in dNA should not be welcomed.

This creationist believes we do have the primate body. We alone don't have a body type for ourselves.This because we alone have our identity in Gods image. Animals identity is in thier kind and so thier body types represent this.We are renting a body type in order to stay in the spectrum of restrictions on the common blueprint for biology.SO I welcome humans being 99'999% alike in DNA with apes/orangs/chimps.We do have ape bodies.We alone in nature are like this.The best beings alone have bodies like other beings.No one else can say that.

If humans were specially created, why did God create us to look more similar to chimpanzees than rats are to mice?

That is subjective. In what way do we look more similar to chimps than rats do to mice? And which rats and mice are you talking about?

If it is genetically, ie we are allegedly more genetically similar to chimps than rats are to mice, we don't have enough information to answer that question.

Why do we look like we share a common ancestor with them?

Another subjective opinion. We don't look like we share a common ancestor with them.

Even if we are really 98%+ similar genetically that small percentage needs to account for a great deal of physiological and morphological change. You would think that such a small % would be easy to map out into those changes. However that has been elusive. So either evolutionary biologists are really dim or the alleged relationship never existed and the genetics means something else entirely.

There's more to a genome than protein coding. These high percentages given are always qualified (not seen in the post here, but clarified in response to my comment above). These numbers shouldn't fool anyone into thinking they might accidentally produce simian offspring.

All these arguings are to divert attention away from this startling fact: something doesn't come from nothing, except supernaturally. Without something to conceive of and create existence, there would be nothing for nothing to exist in, and nobody to observe the nothing, and nobody would be the wiser.

Sirthere is another option for why man looks like primates.it being that we, uniquely, made in Gods image can not have this image represented in the common blueprint of biology. all creatures almost are the same. the same blueprint surely.All creatures , originally, look like they are. We do not. We are mini-Gods, as my pastor put it, So we had to be given the best body, for fun and profit and so the ape one, and yet remain in the spectrum.We should be a perfect copy of apes as they were originally.The bible provides an option.We alone do share like genes with creatures totally unloike us. who else does?

Sirthere is another option for why man looks like primates.it being that we, uniquely, made in Gods image can not have this image represented in the common blueprint of biology. all creatures almost are the same. the same blueprint surely.All creatures , originally, look like they are. We do not. We are mini-Gods, as my pastor put it, So we had to be given the best body, for fun and profit and so the ape one, and yet remain in the spectrum.We should be a perfect copy of apes as they were originally.The bible provides an option.We alone do share like genes with creatures totally unloike us. who else does?

JoshuaThe answer to the puzzle may be other biochemical difference other than the genome. There are large differences in the timing expression and alternative splicing sequences between humans and chimps. Proteins are modified by alternative splicing and 70 to 90% of the human genome is alternatively spliced vs half for a chimp. So that same DNA can produce a very different protein by way of the spliceosome. I can supply papers on this subject if you would like. Unfortunately the source of the splicing codes is not understood at this point but almost certainly are not formed from a stochastic processes. The hypotheses that man evolved from chimps via a stochastic process is almost certainly false.

The design argument does not add much to the party here either. It is simply an inference based on biochemical mechanisms being more likely caused by intelligence vs stochastic processes.

A cogent and kind defense of my position, that rebuts the science in your article, has appeared. It is posted by Vincent Torley from Uncommon Descent. He is another advocate of ID. He gets my article correct, and he has the science correct. If you do not agree, it would be worth hearing your response.

Why do humans and chimps share such similar genomes, while the genomes of humans and mice differ so dramatically (see Mouse Genome Sequencing Consortium 2002)? What is the basis of the pattern of similarity (Wood 2006)?

…Similarity requires explanation, regardless of whether it’s similar genes or similar intergenic DNA.

Torley is out to lunch, IMO. Similarity is a known characteristic of design reuse. In fact, human intelligent design would not exist without it. Any designer who feels the need to reinvent everything is an idiot. Design reuse is so important to human design that software design tools enforce it automatically. It's called object-oriented design. Programmers are encouraged to add functionality through class inheritance. It does not involve common descent but the intelligent reuse of previous classes. That is all. No stochastic mutations and selection.

The similarity of humans to chimps is a sure sign of intelligent design.

How can you be a professor and not know this about design? You also use a ridiculous but common strawman caricature of God:

Of course, adding God back into the picture, anything could have happened. An omnipotent God could have created us 6,000 years ago…

How do you know that God is omnipotent? What is it with atheists and Darwinists that they feel the need to use a creationist understand of God in order to feel superior and make a lame point? Intelligent design obviously implies that one must have intelligence. Why would an omnipotent, omniscient God need intelligence for? Does not intelligence assumes the ability and necessity to learn?

The way I see it, you insulted the intelligence of Christians with your article. Don't be surprised if you get a taste of your own medicine. You people are not nearly as smart as you think you are.

It makes perfect sense that VJTorley would appreciate your article because he is a fundamentalist Christian at heart. He believes in all sorts of fundamentalist nonsense about God (e.g., omniscience and omnipotence) that contradicts his notions of free will and self determination. The man is a walking contradiction.

Having said that, the stupidity of the beliefs of some Christians does not give you a free pass to promote your own nonsense. You cannot use their erroneous stance as a strawman to advance your own erroneous position.

And shared disease-causing mutations indicate common descent because ... why?

For the same reason the shared pattern of ERVs does. That the identical mutations are in the identical place is an indication the mutations occurred before the lineages diverged. Maybe you can get one of the IDers here to calculate the probability that 80 identical SNPs would occur in identical places on two separate lineages independently.

For the same reason the shared pattern of ERVs does. That the identical mutations are in the identical place is an indication the mutations occurred before the lineages diverged. Maybe you can get one of the IDers here to calculate the probability that 80 identical SNPs would occur in identical places on two separate lineages independently.

Let's include all the mutations, including those that are "shared," but with less similar species, such that evolutionists explain them as arising independently. If shared mutations can arise independently, then why are the ones found in similar species interpreted as compelling evidence for CD?

As far as I know the only such rare cases involve beneficial mutations in which similar selection pressures resulted in the same genetic solution being hit upon. Mutations in the prestin gene for example allow detection of the same high frequencies in some bats and some cetaceans, a feature that is very beneficial to both.

Why would your Designer install 80 different disease causing mutations such that the identical ones appear in the identical place in the genomes of two independently created species? Just feeling sadistic that day?

"Er, no. A small handful of the known ERV sequences have picked up a secondary function since they entered the human genome millions of years previously."-

not according to the paper:

"We report the existence of 51,197 ERV-derived promoter sequences that initiate transcription within the human genome, including 1743 cases where transcription is initiated from ERV sequences that are located in gene proximal promoter or 5' untranslated regions (UTRs).

[...]

Our analysis revealed that retroviral sequences in the human genome encode tens-of-thousands of active promoters; transcribed ERV sequences correspond to 1.16% of the human genome sequence and PET tags that capture transcripts initiated from ERVs cover 22.4% of the genome. These data suggest that ERVs may regulate human transcription on a large scale."

so its not few here and there.

plus: what about the possibility of convergent insertion? remember that if most of the genome isnt junk then there is only a small place that erv insertion can happen.

Well "convergent" designs in general are rampant in biology. That alone is problematic for CD.

Convergence isn’t any sort of problem for CD. There are a finite number of solutions to the physics problems faced by life forms. Dolphins and sharks are both streamlined because that’s the most efficient shape for moving quickly through water, not because the Designer likes curves.

it shouldn't be difficult to think of ways that deleterious shared mutations could arise.

Then let’s hear your non-evolutionary explanation for the 80 identical disease causing mutations in identical locations in the chimp and human genomes.

In fact, deleterious shared mutations do not help CD.

Of course they do unless you have a better explanation.

The deleterious shared mutations are not probable on CD, but they are even less probable on the alternative.

No one in science reasons like that but since I know it’s your favorite strawman I’m not surprised you lugged it out again.

How do evolutionists know that there are only two choices

They don’t. It’s the ID-Creationist who are always using the false dichotomy; if ToE is falsified then ID-Creationism must be correct by default. Science is always open to new ideas as ling as they are supported by sufficient positive evidence. Your problem is ID-Creationism has no such positive evidence at all

Um, it might be possible to tangle out a metaphysics that justifies this phenomenon, but many metaphysical models fail on it.

Now, I am a computer programmer. I laugh at many of the arguments presented by evos that "a designer would never do this". When I produce programs, the programs have "junk code", lots of it. I, an intelligent designer, write less than optimal programs pretty much every time. I certainly have to balance between one "optimal" and another every time.

I even write bugs, lots of them.

However, if I am going to write two pieces of code, I am not going to repeatedly put the very same bug in the very same relative place in each program. Now, the bug might just be floating along in a library that I link in at compile time. However, if such a bug is linked in, that means that the master library of code is buggy -- a metaphysically interesting concept.

Well, maybe the designer goes out of his way to produce disease. That challenges a number of metaphysical models.

My personal metaphysical model says that entropy happens -- deleterious mutations. Entropic mutations are passed down from parent to child. All metaphysical models that I can conjure which view disease producing mutations as "not designed", obligate the 80 or so mutations to be in both human and chimp line because they share a common ancestor.

Oh, there is that possibility that the devil engineers disease producing mutations and stick's 'em into species. Maybe the devil sometimes chooses the identical mutation to stick in multiple species. Maybe the devil loves it because it makes things look like UCA. Um, I don't give the devil that much credit.

I think people get the wrong idea about that one that has no need to answer to any man. About this around the species in 80 mutations, wouldn't it be amusing if it was done so just for this very conversation and these very doubts, which people use to justify themselves, so that they might see but not understand?

Joshua"However, Professor Swamidass never claims in his article that human beings originated via a blind process. As I mentioned above, he’s a scientist who is a Christian. His sole aim, in writing the article, was to show creationists that there is a wealth of scientific evidence supporting the claim that human beings and chimpanzees shared a common ancestor. Nothing in that claim stipulates the mechanism whereby humans arose: it may have been a guided process or an unguided one.”

This is from VJ's article. If you agree with him that you are not claiming a stochastic mechanism then we are in sync however I don't think this is common decent what you are claiming is common biochemistry. In my humble opinion common decent implies the process occurred through known natural causes.

JoshuaGot it. "For me common decent is a misleading term because it came with the theory when the mechanism RMNS was assumed. You are claiming common biochemistry which is true but to round out the article differences must also be clearly examined and hopefully this debate will shake them out. While the DNA similarity is very true the splicing differences are the largest among all vertebrates...abstract below.

The Evolutionary Landscape of Alternative Splicing in Vertebrate SpeciesNuno L. Barbosa-Morais1,2, Manuel Irimia1,*, Qun Pan1,*, Hui Y. Xiong3,*, Serge Gueroussov1,4,*,Leo J. Lee3, Valentina Slobodeniuc1, Claudia Kutter5, Stephen Watt5, Recep Çolak1,6, TaeHyung Kim1,7, Christine M. Misquitta-Ali1, Michael D. Wilson4,5,7, Philip M. Kim1,4,6, Duncan T. Odom5,8,Brendan J. Frey1,3, Benjamin J. Blencowe1,4,†Author Affiliations↵†To whom correspondence should be addressed. E-mail: b.blencowe@utoronto.ca ↵* These authors contributed equally to this work.￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼￼+￼￼￼￼￼￼ABSTRACTHow species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning ~350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates. Within 6 million years, the splicing profiles of physiologically equivalent organs diverged such that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species- specific splicing patterns are cis-directed. However, a subset of pronounced splicing changes are predicted to remodel protein interactions involving trans-acting regulators. These events likely further contributed to the diversification of splicing and other transcriptomic changes that underlie phenotypic differences among vertebrate species."

Again, if we are so genetically similar to chimps, ie less than 2^ difference, it should be easy to map the transformations required to the genetics. Yet no one has. So either evolutionary biologists are really, really dim or we do not share a common ancestor with chimps.

He writes, "As predicted by common ancestry, human and chimpanzee genomes are extremely similar (greater than 98% similarity in coding regions)..."

As predicted based on common ancestry by whom? When? Where?

With no documentation of this alleged prediction, it is impossible to credit the man's article above the level of a carnival barker or the penny-stock scamster.

I would like to be surprised that his lack of the most basic scholarly standards would be acceptable at the Laboratory and Genomic Medicine Department of Pathology and Immunology Washington at the University in St. Louis. But I'm not.